EEL mouse sagittal 440 genes spatial RNA data

<strong>Raw RNA locations of a sagittal mouse brain section produced by EEL FISH for 440 genes.</strong> The file contains 11249762 rows and 7 columns. The RNA file is in the .parquet file format which can be opened with FISHscale (https://github.com/linnarsson-lab/FISHscale) or any other parquet file reader (https://arrow.apache.org/docs/index.html). Alternatively, there is also a .csv file with the RNA data. However, it is more that 1GB and the .parquet file will be more efficient. <br> <strong>RNA .parquet or .csv files</strong> Position and gene label for all RNA molecules. "c_px_microscope_stitched" contains X coordinates. "r_px_microscope_stitched" contians Y coordinates. The unit are pixels with a size of 0.18 micrometer. Multiply by 0.18 to get um scale. "c_transformed" contains X coordinates. "r_transformed" contains Y coordinates. The units are pixels with a size of 0.27 micrometer. Multiply by 0.27 to get um scale. These coordinates match the coordinates in the single cell .loom file. "decoded_genes" contains the gene label for each point. Note that there are 8 empty barcodes as negatie controls, labeled "Control1" to "Control8". There is also a gene called "Cre" that is not present in this sample. Please remove controls and Cre before analysing any biological questions. "hamming_distance" is the hamming distance divided by the barcode length (16). The closer to 0 the better the barcode. "Valid" Boolean colum where detected RNA molecules that are inside the tissue section are labeled with a 1. <br> <strong>Tissue polygon .csv file</strong> The .csv flie contains a polygon of the tissue area to clip RNA molecules outside. This was used to generate the "Valid" column. The unit size is in micrometer. <br> <strong>Gene colors .pkl file</strong> Pickled Python dictionary with gene colors used in the paper.